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Author: Oliver G Pybus

Rankings

  • All-time downloads: 150,844 (rank: 977 )
  • Categories:
    • bioinformatics: 2,598 (rank: 7,007 (tie) )
    • ecology: 376 (rank: 15,591 (tie) )
    • epidemiology: 59,074 (rank: 419 )
    • evolutionary biology: 4,437 (rank: 998 )
    • genetics: 2,943 (rank: 7,463 )
    • genomics: 914 (rank: 29,235 (tie) )
    • immunology: 1,415 (rank: 10,887 (tie) )
    • infectious diseases: 65,545 (rank: 1,043 )
    • microbiology: 8,877 (rank: 2,302 (tie) )
    • molecular biology: 919 (rank: 9,236 (tie) )

Downloads per author, site-wide

Preprints

Viral infection and Transmission in a large well-traced outbreak caused by the Delta SARS-CoV-2 variant

epidemiology more details view paper
  • Downloaded 32,149 times
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    • Site-wide: 311
    • In epidemiology: 63
  • Year to date:
    • Site-wide: 1,143
  • Since beginning of last month:
    • Site-wide: 2,652

COVID-19 herd immunity in the Brazilian Amazon

infectious diseases more details view paper
  • Downloaded 29,973 times
  • Download rankings, all-time:
    • Site-wide: 333
    • In infectious diseases: 125
  • Year to date:
    • Site-wide: 5,034
  • Since beginning of last month:
    • Site-wide: 5,676

Early evaluation of the Wuhan City travel restrictions in response to the 2019 novel coronavirus outbreak

infectious diseases more details view paper
  • Downloaded 15,660 times
  • Download rankings, all-time:
    • Site-wide: 720
    • In infectious diseases: 255
  • Year to date:
    • Site-wide: 14,184
  • Since beginning of last month:
    • Site-wide: 16,624

A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

microbiology more details view paper
  • Downloaded 8,994 times
  • Download rankings, all-time:
    • Site-wide: 1,457
    • In microbiology: 131
  • Year to date:
    • Site-wide: 22,965
  • Since beginning of last month:
    • Site-wide: 22,527

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

infectious diseases more details view paper
  • Downloaded 7,090 times
  • Download rankings, all-time:
    • Site-wide: 1,974
    • In infectious diseases: 545
  • Year to date:
    • Site-wide: 50,127
  • Since beginning of last month:
    • Site-wide: 41,044

Evolution and epidemic spread of SARS-CoV-2 in Brazil

infectious diseases more details view paper
  • Downloaded 6,171 times
  • Download rankings, all-time:
    • Site-wide: 2,382
    • In infectious diseases: 626
  • Year to date:
    • Site-wide: 75,811
  • Since beginning of last month:
    • Site-wide: 73,855

The effect of human mobility and control measures on the COVID-19 epidemic in China

epidemiology more details view paper
  • Downloaded 6,170 times
  • Download rankings, all-time:
    • Site-wide: 2,383
    • In epidemiology: 278
  • Year to date:
    • Site-wide: 16,199
  • Since beginning of last month:
    • Site-wide: 15,720

Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China

infectious diseases more details view paper
  • Downloaded 5,613 times
  • Download rankings, all-time:
    • Site-wide: 2,702
    • In infectious diseases: 711
  • Year to date:
    • Site-wide: 1,347
  • Since beginning of last month:
    • Site-wide: 29,003

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

epidemiology more details view paper
  • Downloaded 4,982 times
  • Download rankings, all-time:
    • Site-wide: 3,175
    • In epidemiology: 354
  • Year to date:
    • Site-wide: 5,239
  • Since beginning of last month:
    • Site-wide: 2,889

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.

epidemiology more details view paper
  • Downloaded 2,599 times
  • Download rankings, all-time:
    • Site-wide: 8,055
    • In epidemiology: 645
  • Year to date:
    • Site-wide: 114,098
  • Since beginning of last month:
    • Site-wide: 105,365

Routes for COVID-19 importation in Brazil

epidemiology more details view paper
  • Downloaded 2,413 times
  • Download rankings, all-time:
    • Site-wide: 8,953
    • In epidemiology: 701
  • Year to date:
    • Site-wide: 119,811
  • Since beginning of last month:
    • Site-wide: 96,027

Global disparities in SARS-CoV-2 genomic surveillance

epidemiology more details view paper
  • Downloaded 2,080 times
  • Download rankings, all-time:
    • Site-wide: 11,203
    • In epidemiology: 1,032
  • Year to date:
    • Site-wide: 2,718
  • Since beginning of last month:
    • Site-wide: 4,383

Identification of a common deletion in the spike protein of SARS-CoV-2

genetics more details view paper
  • Downloaded 2,005 times
  • Download rankings, all-time:
    • Site-wide: 11,814
    • In genetics: 436
  • Year to date:
    • Site-wide: 116,704
  • Since beginning of last month:
    • Site-wide: 180,121

Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK

epidemiology more details view paper
  • Downloaded 1,971 times
  • Download rankings, all-time:
    • Site-wide: 12,118
    • In epidemiology: 895
  • Year to date:
    • Site-wide: 70,952
  • Since beginning of last month:
    • Site-wide: 50,054

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

epidemiology more details view paper
  • Downloaded 1,817 times
  • Download rankings, all-time:
    • Site-wide: 13,643
    • In epidemiology: 955
  • Year to date:
    • Site-wide: 174,018
  • Since beginning of last month:
    • Site-wide: 160,246

Discovery of a persistent Zika virus lineage in Bahia, Brazil

epidemiology more details view paper
  • Downloaded 1,267 times
  • Download rankings, all-time:
    • Site-wide: 23,726
    • In epidemiology: 1,382
  • Year to date:
    • Site-wide: 179,144
  • Since beginning of last month:
    • Site-wide: 148,252

Epidemiological and ecological determinants of Zika virus transmission in an urban setting.

epidemiology more details view paper
  • Downloaded 1,246 times
  • Download rankings, all-time:
    • Site-wide: 24,370
    • In epidemiology: 1,417
  • Year to date:
    • Site-wide: 129,864
  • Since beginning of last month:
    • Site-wide: 140,530

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

evolutionary biology more details view paper
  • Downloaded 1,209 times
  • Download rankings, all-time:
    • Site-wide: 25,511
    • In evolutionary biology: 881
  • Year to date:
    • Site-wide: 90,889
  • Since beginning of last month:
    • Site-wide: 109,077

Epidemiology of the Zika virus outbreak in the Cabo Verde Islands, West Africa

epidemiology more details view paper
  • Downloaded 1,170 times
  • Download rankings, all-time:
    • Site-wide: 26,807
    • In epidemiology: 1,508
  • Year to date:
    • Site-wide: 139,718
  • Since beginning of last month:
    • Site-wide: 142,673

Vaccine nationalism and the dynamics and control of SARS-CoV-2

epidemiology more details view paper
  • Downloaded 1,145 times
  • Download rankings, all-time:
    • Site-wide: 27,739
    • In epidemiology: 1,614
  • Year to date:
    • Site-wide: 44,235
  • Since beginning of last month:
    • Site-wide: 69,369

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

epidemiology more details view paper
  • Downloaded 1,116 times
  • Download rankings, all-time:
    • Site-wide: 28,825
    • In epidemiology: 1,599
  • Year to date:
    • Site-wide: 143,153
  • Since beginning of last month:
    • Site-wide: 144,215

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

infectious diseases more details view paper
  • Downloaded 1,090 times
  • Download rankings, all-time:
    • Site-wide: 29,889
    • In infectious diseases: 2,909
  • Year to date:
    • Site-wide: 19,150
  • Since beginning of last month:
    • Site-wide: 13,092

Parallel Evolution in the Emergence of Highly Pathogenic Avian Influenza A Viruses

evolutionary biology more details view paper
  • Downloaded 968 times
  • Download rankings, all-time:
    • Site-wide: 35,635
    • In evolutionary biology: 1,369
  • Year to date:
    • Site-wide: 117,899
  • Since beginning of last month:
    • Site-wide: 117,409

Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structures

molecular biology more details view paper
  • Downloaded 935 times
  • Download rankings, all-time:
    • Site-wide: 37,570
    • In molecular biology: 962
  • Year to date:
    • Site-wide: 149,414
  • Since beginning of last month:
    • Site-wide: 159,733

Human B cell lineages engaged by germinal centers following influenza vaccination are measurably evolving

immunology more details view paper
  • Downloaded 865 times
  • Download rankings, all-time:
    • Site-wide: 42,099
    • In immunology: 1,483
  • Year to date:
    • Site-wide: 38,401
  • Since beginning of last month:
    • Site-wide: 14,451

Optimal Point Process Filtering and Estimation of the Coalescent Process

bioinformatics more details view paper
  • Downloaded 810 times
  • Download rankings, all-time:
    • Site-wide: 46,394
    • In bioinformatics: 4,458
  • Year to date:
    • Site-wide: 140,171
  • Since beginning of last month:
    • Site-wide: 187,850

Serial Interval Distribution of SARS-CoV-2 Infection in Brazil

infectious diseases more details view paper
  • Downloaded 748 times
  • Download rankings, all-time:
    • Site-wide: 52,130
    • In infectious diseases: 3,545
  • Year to date:
    • Site-wide: 75,713
  • Since beginning of last month:
    • Site-wide: 85,000

Identification of site-specific evolutionary trajectories shared across human betacoronaviruses

evolutionary biology more details view paper
  • Downloaded 705 times
  • Download rankings, all-time:
    • Site-wide: 56,546
    • In evolutionary biology: 2,751
  • Year to date:
    • Site-wide: 50,415
  • Since beginning of last month:
    • Site-wide: 97,456

Optimal Point Process Filtering for Birth-Death Model Estimation

bioinformatics more details view paper
  • Downloaded 671 times
  • Download rankings, all-time:
    • Site-wide: 60,645
    • In bioinformatics: 5,560
  • Year to date:
    • Site-wide: 165,088
  • Since beginning of last month:
    • Site-wide: 177,446

A computationally tractable birth-death model that combines phylogenetic and epidemiological data

genomics more details view paper
  • Downloaded 658 times
  • Download rankings, all-time:
    • Site-wide: 62,223
    • In genomics: 4,236
  • Year to date:
    • Site-wide: 89,066
  • Since beginning of last month:
    • Site-wide: 128,914

Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination

immunology more details view paper
  • Downloaded 652 times
  • Download rankings, all-time:
    • Site-wide: 62,980
    • In immunology: 1,829
  • Year to date:
    • Site-wide: 170,518
  • Since beginning of last month:
    • Site-wide: 160,395

The multifurcating skyline plot

bioinformatics more details view paper
  • Downloaded 616 times
  • Download rankings, all-time:
    • Site-wide: 67,875
    • In bioinformatics: 6,221
  • Year to date:
    • Site-wide: 133,425
  • Since beginning of last month:
    • Site-wide: 76,372

Robust Design for Coalescent Model Inference

bioinformatics more details view paper
  • Downloaded 577 times
  • Download rankings, all-time:
    • Site-wide: 73,721
    • In bioinformatics: 6,519
  • Year to date:
    • Site-wide: 150,071
  • Since beginning of last month:
    • Site-wide: 114,498

Emergence and persistence of the Chikungunya virus East-Central-South-African genotype in Northeast Brazil

epidemiology more details view paper
  • Downloaded 563 times
  • Download rankings, all-time:
    • Site-wide: 75,952
    • In epidemiology: 3,268
  • Year to date:
    • Site-wide: 143,997
  • Since beginning of last month:
    • Site-wide: 160,237

The evolutionary dynamics of Oropouche Virus (OROV) in South America

evolutionary biology more details view paper
  • Downloaded 559 times
  • Download rankings, all-time:
    • Site-wide: 76,622
    • In evolutionary biology: 3,440
  • Year to date:
    • Site-wide: 166,385
  • Since beginning of last month:
    • Site-wide: 139,327

Seasonal dynamics of the wild rodent faecal virome

ecology more details view paper
  • Downloaded 553 times
  • Download rankings, all-time:
    • Site-wide: 77,522
    • In ecology: 2,945
  • Year to date:
    • Site-wide: 4,240
  • Since beginning of last month:
    • Site-wide: 16,357

Jointly inferring the dynamics of population size and sampling intensity from molecular sequences

genetics more details view paper
  • Downloaded 551 times
  • Download rankings, all-time:
    • Site-wide: 77,900
    • In genetics: 3,040
  • Year to date:
    • Site-wide: 125,977
  • Since beginning of last month:
    • Site-wide: 149,141

Modelling the decay of hotspot motifs in broadly neutralizing antibody lineages

evolutionary biology more details view paper
  • Downloaded 487 times
  • Download rankings, all-time:
    • Site-wide: 90,126
    • In evolutionary biology: 4,008
  • Year to date:
    • Site-wide: 187,984
  • Since beginning of last month:
    • Site-wide: 178,120

Are skyline plot-based demographic estimates overly dependent on smoothing prior assumptions?

genetics more details view paper
  • Downloaded 447 times
  • Download rankings, all-time:
    • Site-wide: 98,955
    • In genetics: 3,773
  • Year to date:
    • Site-wide: 152,292
  • Since beginning of last month:
    • Site-wide: 127,804

High resolution evolutionary analysis of within-host hepatitis C virus infection

evolutionary biology more details view paper
  • Downloaded 381 times
  • Download rankings, all-time:
    • Site-wide: 115,134
    • In evolutionary biology: 5,239
  • Year to date:
    • Site-wide: 173,031
  • Since beginning of last month:
    • Site-wide: 132,714

Oropouche virus cases identified in Ecuador using an optimised rRT-PCR informed by metagenomic sequencing

genomics more details view paper
  • Downloaded 296 times
  • Download rankings, all-time:
    • Site-wide: 139,188
    • In genomics: 7,114
  • Year to date:
    • Site-wide: 144,089
  • Since beginning of last month:
    • Site-wide: 113,070

Kankasha in Kassala: a prospective observational cohort study of the clinical characteristics, epidemiology, genetic origin, and chronic impact of the 2018 epidemic of Chikungunya virus infection in Kassala, Sudan

infectious diseases more details view paper
  • Downloaded 255 times
  • Download rankings, all-time:
    • Site-wide: 151,495
    • In infectious diseases: 6,367
  • Year to date:
    • Site-wide: 119,201
  • Since beginning of last month:
    • Site-wide: 89,478

Discovery of Flaviviridae-derived endogenous viral elements in shrew genomes provide novel insights into Pestivirus ancient history

microbiology more details view paper
  • Downloaded 222 times
  • Download rankings, all-time:
    • Site-wide: 160,993
    • In microbiology: None
  • Year to date:
    • Site-wide: 16,703
  • Since beginning of last month:
    • Site-wide: 51,297

Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

evolutionary biology more details view paper
  • Downloaded 218 times
  • Download rankings, all-time:
    • Site-wide: 161,965
    • In evolutionary biology: 7,869
  • Year to date:
    • Site-wide: 32,718
  • Since beginning of last month:
    • Site-wide: 36,136

Global prevalence and phylogeny of hepatitis B virus (HBV) drug and vaccine resistance mutations

evolutionary biology more details view paper
  • Downloaded 177 times
  • Download rankings, all-time:
    • Site-wide: 172,305
    • In evolutionary biology: 7,550
  • Year to date:
    • Site-wide: 148,084
  • Since beginning of last month:
    • Site-wide: 125,602

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